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Ruthenium in PDB 8pfu: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A, PDB code: 8pfu was solved by A.Teran, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.20 / 1.18
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.06, 78.06, 37.47, 90, 90, 90
R / Rfree (%) 17.9 / 20.2

Other elements in 8pfu:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A also contains other interesting chemical elements:

Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A (pdb code 8pfu). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 8 binding sites of Ruthenium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A, PDB code: 8pfu:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Ruthenium binding site 1 out of 8 in 8pfu

Go back to Ruthenium Binding Sites List in 8pfu
Ruthenium binding site 1 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru209

b:63.6
occ:0.40
 RU1 A:YJT209 0.0 63.6 0.4
O1 A:CO3213 2.1 30.5 0.3
O A:LEU129 2.2 39.4 1.0
RU2 A:YJT209 2.3 42.8 0.4
C A:CO3213 3.0 31.1 0.3
O3 A:CO3213 3.1 29.3 0.3
C A:LEU129 3.3 37.3 1.0
OXT A:LEU129 3.7 40.9 1.0
O2 A:CO3213 4.2 31.9 0.3
CA A:LEU129 4.6 28.0 1.0
N A:LEU129 4.6 26.5 1.0

Ruthenium binding site 2 out of 8 in 8pfu

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Ruthenium binding site 2 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru209

b:42.8
occ:0.40
 RU2 A:YJT209 0.0 42.8 0.4
O3 A:CO3213 2.2 29.3 0.3
OXT A:LEU129 2.2 40.9 1.0
RU1 A:YJT209 2.3 63.6 0.4
O A:LEU129 2.5 39.4 1.0
C A:LEU129 2.7 37.3 1.0
C A:CO3213 2.9 31.1 0.3
O1 A:CO3213 3.0 30.5 0.3
O2 A:CO3213 4.1 31.9 0.3
CA A:LEU129 4.2 28.0 1.0
CE A:LYS13 4.6 36.0 1.0
CB A:LEU129 4.9 28.9 1.0
N A:LEU129 4.9 26.5 1.0

Ruthenium binding site 3 out of 8 in 8pfu

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Ruthenium binding site 3 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru210

b:40.2
occ:0.20
 RU1 A:YJT210 0.0 40.2 0.2
OD1 A:ASN103 2.2 39.5 0.7
RU2 A:YJT210 2.3 40.6 0.2
O A:HOH435 3.2 33.8 1.0
CG A:ASN103 3.2 32.1 0.7
RU2 A:YJT211 3.3 36.1 0.2
O A:ASP101 3.5 28.5 0.5
OD2 A:ASP101 3.7 35.3 0.5
ND2 A:ASN103 3.7 34.9 0.7
O A:ASP101 4.1 23.4 0.5
OD1 A:ASP101 4.3 18.9 0.5
CB A:ASN103 4.4 26.9 0.7
CB A:ASN103 4.4 19.3 0.3
N A:ASN103 4.5 20.0 0.3
CG A:ASP101 4.5 30.4 0.5
N A:ASN103 4.5 21.1 0.7
C A:ASP101 4.6 26.6 0.5
CG A:ASP101 4.6 21.2 0.5
C A:ASP101 4.7 27.0 0.5
CA A:GLY102 4.8 24.5 1.0
C A:GLY102 4.8 21.9 1.0
OD2 A:ASP101 4.9 21.9 0.5
CA A:ASN103 4.9 17.9 0.3
O A:HOH302 5.0 31.5 1.0

Ruthenium binding site 4 out of 8 in 8pfu

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Ruthenium binding site 4 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru210

b:40.6
occ:0.20
 RU2 A:YJT210 0.0 40.6 0.2
OD1 A:ASN103 2.1 39.5 0.7
ND2 A:ASN103 2.3 34.9 0.7
RU1 A:YJT210 2.3 40.2 0.2
CG A:ASN103 2.5 32.1 0.7
O A:HOH435 2.5 33.8 1.0
CB A:ASN103 4.0 26.9 0.7
CB A:ASN103 4.3 19.3 0.3
CG A:ASN103 4.4 21.8 0.3
OD1 A:ASN103 4.6 24.4 0.3
CA A:ASN103 4.8 17.9 0.3
CA A:ASN103 4.8 20.1 0.7
N A:ASN103 4.9 21.1 0.7
N A:ASN103 4.9 20.0 0.3
ND2 A:ASN103 4.9 24.2 0.3

Ruthenium binding site 5 out of 8 in 8pfu

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Ruthenium binding site 5 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru211

b:36.0
occ:0.20
 RU1 A:YJT211 0.0 36.0 0.2
RU2 A:YJT211 2.3 36.1 0.2
OD1 A:ASP101 2.6 33.2 0.5
OD2 A:ASP101 3.2 35.3 0.5
CG A:ASP101 3.2 30.4 0.5
O A:HOH345 4.0 42.6 1.0
CB A:ASP101 4.4 22.2 0.5
O A:ASP101 4.6 28.5 0.5
O A:ASP101 4.7 23.4 0.5
CB A:ASP101 4.7 26.8 0.5
OD2 A:ASP101 4.8 21.9 0.5
CG A:ASP101 4.8 21.2 0.5

Ruthenium binding site 6 out of 8 in 8pfu

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Ruthenium binding site 6 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 6 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru211

b:36.1
occ:0.20
 RU2 A:YJT211 0.0 36.1 0.2
RU1 A:YJT211 2.3 36.0 0.2
OD2 A:ASP101 2.4 35.3 0.5
CG A:ASP101 3.2 30.4 0.5
RU1 A:YJT210 3.3 40.2 0.2
OD1 A:ASP101 3.5 33.2 0.5
OD2 A:ASP101 4.1 21.9 0.5
O A:ASP101 4.1 28.5 0.5
CG A:ASP101 4.4 21.2 0.5
O A:ASP101 4.6 23.4 0.5
CB A:ASP101 4.6 26.8 0.5
CB A:ASP101 4.6 22.2 0.5
OD1 A:ASP101 4.9 18.9 0.5

Ruthenium binding site 7 out of 8 in 8pfu

Go back to Ruthenium Binding Sites List in 8pfu
Ruthenium binding site 7 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 7 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru212

b:31.3
occ:0.20
 RU1 A:YJT212 0.0 31.3 0.2
RU2 A:YJT212 2.3 29.0 0.2
O A:HOH430 3.7 31.1 1.0
O A:HOH355 3.9 21.2 1.0
O A:HOH373 4.1 27.3 1.0
O A:ASP119 4.8 21.7 1.0

Ruthenium binding site 8 out of 8 in 8pfu

Go back to Ruthenium Binding Sites List in 8pfu
Ruthenium binding site 8 out of 8 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 8 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K3[RU2(CO3)4] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru212

b:29.0
occ:0.20
 RU2 A:YJT212 0.0 29.0 0.2
RU1 A:YJT212 2.3 31.3 0.2
CB A:ALA122 3.9 21.1 1.0
OD2 A:ASP119 4.7 37.5 1.0
O A:HOH306 4.8 49.2 1.0
O A:ASP119 4.9 21.7 1.0

Reference:

S.Herrero Dominguez, A.Teran, G.Ferraro, A.E.Sanchez-Pelaez, A.Merlino. Charge Effect in Protein Metalation Reactions By Diruthenium Complexes Inorg Chem Front 2023.
DOI: 10.1039/D3QI01192E
Page generated: Thu Oct 10 13:14:08 2024

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